Starting phenix.real_space_refine on Wed Mar 4 06:22:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lhg_23339/03_2026/7lhg_23339.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lhg_23339/03_2026/7lhg_23339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lhg_23339/03_2026/7lhg_23339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lhg_23339/03_2026/7lhg_23339.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lhg_23339/03_2026/7lhg_23339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lhg_23339/03_2026/7lhg_23339.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 7299 2.51 5 N 2024 2.21 5 O 2237 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11592 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 6217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6217 Classifications: {'peptide': 805} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 31, 'TRANS': 773} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASP:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1702 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 16, 'TRANS': 198} Chain: "K" Number of atoms: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1177 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 146} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2496 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 299} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 2.52, per 1000 atoms: 0.22 Number of scatterers: 11592 At special positions: 0 Unit cell: (99.813, 96.726, 171.843, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 2237 8.00 N 2024 7.00 C 7299 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 574.2 milliseconds 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2700 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 28 sheets defined 4.2% alpha, 38.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'C' and resid 19 through 25 Processing helix chain 'C' and resid 72 through 78 removed outlier: 3.587A pdb=" N VAL C 76 " --> pdb=" O THR C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.658A pdb=" N LEU C 126 " --> pdb=" O GLN C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 459 removed outlier: 4.111A pdb=" N TYR C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 127 through 132 removed outlier: 3.632A pdb=" N ASP D 130 " --> pdb=" O VAL D 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 158 Processing helix chain 'G' and resid 194 through 200 Processing helix chain 'G' and resid 232 through 237 Processing sheet with id=AA1, first strand: chain 'C' and resid 31 through 32 removed outlier: 3.730A pdb=" N TYR C 32 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE C 50 " --> pdb=" O TYR C 32 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL C 53 " --> pdb=" O GLN C 68 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLN C 68 " --> pdb=" O VAL C 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 41 through 42 removed outlier: 6.609A pdb=" N ASP C 35 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ILE C 119 " --> pdb=" O ASP C 35 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE C 37 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 116 " --> pdb=" O ASP C 111 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP C 111 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG C 118 " --> pdb=" O ARG C 109 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP C 107 " --> pdb=" O ASN C 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 467 through 469 removed outlier: 6.727A pdb=" N THR C 494 " --> pdb=" O LYS C 468 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 473 " --> pdb=" O TYR C 490 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TYR C 471 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR C 472 " --> pdb=" O ALA C 439 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA C 439 " --> pdb=" O THR C 472 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR C 474 " --> pdb=" O THR C 437 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG C 414 " --> pdb=" O ILE C 410 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE C 410 " --> pdb=" O ARG C 414 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR C 398 " --> pdb=" O SER C 426 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLY C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 393 " --> pdb=" O GLY C 397 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR C 382 " --> pdb=" O ALA C 379 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY C 343 " --> pdb=" O PHE C 357 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TYR C 338 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRP C 239 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE C 231 " --> pdb=" O TRP C 239 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR C 241 " --> pdb=" O ASN C 229 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN C 229 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE C 217 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N PHE C 211 " --> pdb=" O GLU C 228 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N ASN C 230 " --> pdb=" O SER C 209 " (cutoff:3.500A) removed outlier: 14.993A pdb=" N SER C 209 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU C 192 " --> pdb=" O ASN C 203 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN C 205 " --> pdb=" O SER C 190 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASP C 186 " --> pdb=" O SER C 209 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE C 211 " --> pdb=" O ARG C 184 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ARG C 184 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU C 213 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ARG C 182 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN C 153 " --> pdb=" O SER C 169 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN C 151 " --> pdb=" O ASN C 171 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR C 634 " --> pdb=" O ALA C 641 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 641 through 643 removed outlier: 3.604A pdb=" N THR C 634 " --> pdb=" O ALA C 641 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER C 579 " --> pdb=" O SER C 603 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 594 through 595 Processing sheet with id=AA6, first strand: chain 'C' and resid 594 through 595 removed outlier: 3.665A pdb=" N SER C 588 " --> pdb=" O TYR C 563 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR C 563 " --> pdb=" O SER C 588 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C 529 " --> pdb=" O ASN C 536 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER C 491 " --> pdb=" O TYR C 503 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR C 494 " --> pdb=" O LYS C 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 265 through 266 removed outlier: 4.040A pdb=" N GLY C 266 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE C 293 " --> pdb=" O GLY C 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 277 removed outlier: 4.190A pdb=" N SER C 277 " --> pdb=" O ASP C 307 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP C 307 " --> pdb=" O SER C 277 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU C 306 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL C 322 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 308 " --> pdb=" O PHE C 320 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE C 320 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS C 318 " --> pdb=" O VAL C 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 677 through 680 removed outlier: 3.710A pdb=" N GLY C 719 " --> pdb=" O ARG C 652 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG C 721 " --> pdb=" O LEU C 654 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 689 through 690 removed outlier: 3.542A pdb=" N ASN C 689 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER C 711 " --> pdb=" O ASN C 689 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'C' and resid 730 through 732 Processing sheet with id=AB4, first strand: chain 'C' and resid 756 through 758 removed outlier: 3.642A pdb=" N GLY C 758 " --> pdb=" O VAL C 749 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL C 779 " --> pdb=" O GLN C 786 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN C 786 " --> pdb=" O VAL C 779 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TRP C 781 " --> pdb=" O LYS C 784 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 2 through 4 removed outlier: 3.568A pdb=" N SER D 3 " --> pdb=" O SER D 23 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 8 through 12 removed outlier: 6.542A pdb=" N ALA D 9 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ARG D 116 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N PHE D 11 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 56 through 59 removed outlier: 3.624A pdb=" N GLN D 57 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU D 32 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR D 109 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLU D 92 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU D 107 " --> pdb=" O GLU D 92 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL D 102 " --> pdb=" O ALA K 169 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ALA K 171 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLN D 104 " --> pdb=" O ALA K 171 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N PHE K 173 " --> pdb=" O GLN D 104 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA D 106 " --> pdb=" O PHE K 173 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU K 175 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLN D 108 " --> pdb=" O LEU K 175 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N TYR K 177 " --> pdb=" O GLN D 108 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LYS D 110 " --> pdb=" O TYR K 177 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR K 176 " --> pdb=" O THR K 85 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 50 through 52 removed outlier: 4.076A pdb=" N ILE D 51 " --> pdb=" O SER D 70 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 177 through 181 removed outlier: 3.699A pdb=" N SER D 177 " --> pdb=" O ASN D 145 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE D 133 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 171 through 172 removed outlier: 3.850A pdb=" N VAL D 171 " --> pdb=" O VAL D 153 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL D 153 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR D 152 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE D 194 " --> pdb=" O THR D 152 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N SER D 192 " --> pdb=" O ILE D 154 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 66 through 70 removed outlier: 3.772A pdb=" N GLU K 66 " --> pdb=" O ALA K 148 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA K 148 " --> pdb=" O GLU K 66 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 110 through 112 Processing sheet with id=AC4, first strand: chain 'G' and resid 57 through 61 removed outlier: 6.914A pdb=" N PHE G 26 " --> pdb=" O THR G 60 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN G 180 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE G 81 " --> pdb=" O GLN G 180 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS G 182 " --> pdb=" O GLU G 79 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU G 79 " --> pdb=" O HIS G 182 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA G 184 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR G 77 " --> pdb=" O ALA G 184 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG G 78 " --> pdb=" O ASP G 128 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP G 128 " --> pdb=" O ARG G 78 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS G 126 " --> pdb=" O TYR G 80 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ALA G 82 " --> pdb=" O GLY G 124 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY G 124 " --> pdb=" O ALA G 82 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL G 84 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LEU G 122 " --> pdb=" O VAL G 84 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE G 120 " --> pdb=" O GLU G 111 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 57 through 61 removed outlier: 6.914A pdb=" N PHE G 26 " --> pdb=" O THR G 60 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN G 180 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE G 81 " --> pdb=" O GLN G 180 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS G 182 " --> pdb=" O GLU G 79 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU G 79 " --> pdb=" O HIS G 182 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA G 184 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR G 77 " --> pdb=" O ALA G 184 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 33 through 40 removed outlier: 3.578A pdb=" N TYR G 35 " --> pdb=" O LEU G 208 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU G 210 " --> pdb=" O TYR G 35 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N LYS G 212 " --> pdb=" O GLY G 37 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASN G 39 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE G 211 " --> pdb=" O TYR G 169 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 47 through 49 removed outlier: 3.600A pdb=" N GLU G 101 " --> pdb=" O LYS G 157 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 240 through 241 Processing sheet with id=AC9, first strand: chain 'G' and resid 240 through 241 Processing sheet with id=AD1, first strand: chain 'G' and resid 256 through 261 removed outlier: 3.523A pdb=" N ARG G 256 " --> pdb=" O ILE G 334 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR G 330 " --> pdb=" O LEU G 260 " (cutoff:3.500A) 340 hydrogen bonds defined for protein. 915 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.98 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3737 1.34 - 1.46: 2826 1.46 - 1.58: 5240 1.58 - 1.70: 2 1.70 - 1.83: 52 Bond restraints: 11857 Sorted by residual: bond pdb=" C THR D 71 " pdb=" N THR D 72 " ideal model delta sigma weight residual 1.327 1.480 -0.153 1.71e-02 3.42e+03 8.01e+01 bond pdb=" C LYS D 77 " pdb=" N LEU D 78 " ideal model delta sigma weight residual 1.328 1.398 -0.070 1.14e-02 7.69e+03 3.80e+01 bond pdb=" CA LEU C 86 " pdb=" CB LEU C 86 " ideal model delta sigma weight residual 1.527 1.599 -0.072 1.75e-02 3.27e+03 1.70e+01 bond pdb=" C VAL C 288 " pdb=" N PRO C 289 " ideal model delta sigma weight residual 1.330 1.373 -0.043 1.25e-02 6.40e+03 1.18e+01 bond pdb=" CA CYS K 75 " pdb=" C CYS K 75 " ideal model delta sigma weight residual 1.522 1.565 -0.042 1.37e-02 5.33e+03 9.62e+00 ... (remaining 11852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.85: 15715 4.85 - 9.70: 354 9.70 - 14.55: 35 14.55 - 19.40: 2 19.40 - 24.25: 1 Bond angle restraints: 16107 Sorted by residual: angle pdb=" N ILE C 235 " pdb=" CA ILE C 235 " pdb=" C ILE C 235 " ideal model delta sigma weight residual 111.62 100.76 10.86 7.90e-01 1.60e+00 1.89e+02 angle pdb=" C THR D 71 " pdb=" N THR D 72 " pdb=" CA THR D 72 " ideal model delta sigma weight residual 123.15 147.40 -24.25 2.23e+00 2.01e-01 1.18e+02 angle pdb=" C TYR K 58 " pdb=" N PRO K 59 " pdb=" CA PRO K 59 " ideal model delta sigma weight residual 120.38 131.09 -10.71 1.03e+00 9.43e-01 1.08e+02 angle pdb=" N ASN C 368 " pdb=" CA ASN C 368 " pdb=" C ASN C 368 " ideal model delta sigma weight residual 110.44 99.09 11.35 1.20e+00 6.94e-01 8.94e+01 angle pdb=" CA TYR C 26 " pdb=" CB TYR C 26 " pdb=" CG TYR C 26 " ideal model delta sigma weight residual 113.90 130.59 -16.69 1.80e+00 3.09e-01 8.60e+01 ... (remaining 16102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 6140 17.08 - 34.16: 681 34.16 - 51.24: 145 51.24 - 68.32: 28 68.32 - 85.40: 14 Dihedral angle restraints: 7008 sinusoidal: 2749 harmonic: 4259 Sorted by residual: dihedral pdb=" C ASP C 481 " pdb=" N ASP C 481 " pdb=" CA ASP C 481 " pdb=" CB ASP C 481 " ideal model delta harmonic sigma weight residual -122.60 -133.64 11.04 0 2.50e+00 1.60e-01 1.95e+01 dihedral pdb=" N ASP C 481 " pdb=" C ASP C 481 " pdb=" CA ASP C 481 " pdb=" CB ASP C 481 " ideal model delta harmonic sigma weight residual 122.80 132.58 -9.78 0 2.50e+00 1.60e-01 1.53e+01 dihedral pdb=" C VAL C 7 " pdb=" N VAL C 7 " pdb=" CA VAL C 7 " pdb=" CB VAL C 7 " ideal model delta harmonic sigma weight residual -122.00 -130.96 8.96 0 2.50e+00 1.60e-01 1.28e+01 ... (remaining 7005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1295 0.084 - 0.168: 362 0.168 - 0.252: 66 0.252 - 0.336: 19 0.336 - 0.419: 5 Chirality restraints: 1747 Sorted by residual: chirality pdb=" CA CYS D 207 " pdb=" N CYS D 207 " pdb=" C CYS D 207 " pdb=" CB CYS D 207 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" CB ILE D 194 " pdb=" CA ILE D 194 " pdb=" CG1 ILE D 194 " pdb=" CG2 ILE D 194 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CA TRP C 92 " pdb=" N TRP C 92 " pdb=" C TRP C 92 " pdb=" CB TRP C 92 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 1744 not shown) Planarity restraints: 2112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 72 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO D 73 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO D 73 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO D 73 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 327 " 0.061 5.00e-02 4.00e+02 9.26e-02 1.37e+01 pdb=" N PRO C 328 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO C 328 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 328 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 698 " -0.055 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO C 699 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 699 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 699 " -0.045 5.00e-02 4.00e+02 ... (remaining 2109 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 3558 2.84 - 3.35: 9196 3.35 - 3.87: 19317 3.87 - 4.38: 19881 4.38 - 4.90: 35363 Nonbonded interactions: 87315 Sorted by model distance: nonbonded pdb=" O ASN G 196 " pdb=" OG1 THR G 200 " model vdw 2.325 3.040 nonbonded pdb=" OG1 THR C 72 " pdb=" OD1 ASP C 74 " model vdw 2.334 3.040 nonbonded pdb=" OG SER C 612 " pdb=" OG SER C 628 " model vdw 2.340 3.040 nonbonded pdb=" OG SER D 159 " pdb=" OE1 GLN D 162 " model vdw 2.345 3.040 nonbonded pdb=" O VAL C 1 " pdb=" OG SER C 22 " model vdw 2.353 3.040 ... (remaining 87310 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.430 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.153 11857 Z= 0.394 Angle : 1.665 24.249 16107 Z= 1.009 Chirality : 0.084 0.419 1747 Planarity : 0.009 0.104 2112 Dihedral : 14.921 85.404 4308 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.26 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 14.72 % Favored : 85.28 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.42 (0.17), residues: 1482 helix: -4.64 (0.30), residues: 52 sheet: -2.41 (0.20), residues: 530 loop : -3.30 (0.15), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG G 78 TYR 0.038 0.004 TYR K 58 PHE 0.045 0.004 PHE G 209 TRP 0.026 0.003 TRP C 781 HIS 0.026 0.004 HIS K 36 Details of bonding type rmsd covalent geometry : bond 0.00789 (11857) covalent geometry : angle 1.66526 (16107) hydrogen bonds : bond 0.28354 ( 323) hydrogen bonds : angle 11.50063 ( 915) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 470 MET cc_start: 0.8237 (ttp) cc_final: 0.7484 (tmm) REVERT: C 790 ASN cc_start: 0.8581 (t0) cc_final: 0.8339 (t0) REVERT: D 7 THR cc_start: 0.8834 (t) cc_final: 0.8633 (m) REVERT: D 87 TYR cc_start: 0.8365 (m-10) cc_final: 0.8145 (m-10) REVERT: D 193 TYR cc_start: 0.8469 (p90) cc_final: 0.8221 (p90) REVERT: D 212 CYS cc_start: 0.8349 (p) cc_final: 0.8005 (p) REVERT: K 30 LEU cc_start: 0.8478 (tp) cc_final: 0.7937 (mp) REVERT: K 66 GLU cc_start: 0.8658 (tp30) cc_final: 0.8400 (tp30) REVERT: K 101 LYS cc_start: 0.9054 (mttm) cc_final: 0.8849 (mmmm) REVERT: K 112 ILE cc_start: 0.9137 (mm) cc_final: 0.8620 (mp) REVERT: K 130 ASN cc_start: 0.8571 (m-40) cc_final: 0.8301 (p0) REVERT: K 174 GLU cc_start: 0.6869 (pm20) cc_final: 0.6304 (pm20) REVERT: G 84 VAL cc_start: 0.7642 (t) cc_final: 0.7380 (t) REVERT: G 269 HIS cc_start: 0.4732 (m-70) cc_final: 0.4445 (m90) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.1222 time to fit residues: 43.4920 Evaluate side-chains 167 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 0.0020 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 ASN ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.117631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.095088 restraints weight = 35267.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.098156 restraints weight = 18352.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.100119 restraints weight = 11725.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.101448 restraints weight = 8624.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.102242 restraints weight = 6982.178| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 11857 Z= 0.174 Angle : 0.755 12.925 16107 Z= 0.398 Chirality : 0.047 0.212 1747 Planarity : 0.006 0.088 2112 Dihedral : 5.028 69.281 1650 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.90 % Allowed : 18.99 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.72 (0.19), residues: 1482 helix: -3.70 (0.46), residues: 48 sheet: -2.06 (0.20), residues: 597 loop : -2.76 (0.18), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 446 TYR 0.023 0.002 TYR C 471 PHE 0.024 0.002 PHE G 209 TRP 0.023 0.002 TRP C 92 HIS 0.013 0.002 HIS G 239 Details of bonding type rmsd covalent geometry : bond 0.00373 (11857) covalent geometry : angle 0.75544 (16107) hydrogen bonds : bond 0.05015 ( 323) hydrogen bonds : angle 7.99556 ( 915) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 338 TYR cc_start: 0.8989 (p90) cc_final: 0.8757 (p90) REVERT: C 470 MET cc_start: 0.8147 (ttp) cc_final: 0.7378 (tmm) REVERT: C 790 ASN cc_start: 0.8681 (t0) cc_final: 0.8462 (t0) REVERT: D 87 TYR cc_start: 0.8708 (m-10) cc_final: 0.8409 (m-10) REVERT: D 121 LYS cc_start: 0.9223 (tttt) cc_final: 0.8863 (tptt) REVERT: K 30 LEU cc_start: 0.8872 (tp) cc_final: 0.8270 (mt) REVERT: K 66 GLU cc_start: 0.8867 (tp30) cc_final: 0.8588 (tp30) REVERT: K 112 ILE cc_start: 0.9147 (mm) cc_final: 0.8752 (mp) REVERT: K 130 ASN cc_start: 0.8533 (m-40) cc_final: 0.8288 (p0) REVERT: K 149 TYR cc_start: 0.8731 (p90) cc_final: 0.7849 (p90) REVERT: G 83 TRP cc_start: 0.7728 (t-100) cc_final: 0.7389 (t-100) REVERT: G 230 ASP cc_start: 0.6538 (t0) cc_final: 0.6044 (t0) outliers start: 36 outliers final: 20 residues processed: 202 average time/residue: 0.0989 time to fit residues: 28.5741 Evaluate side-chains 178 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 209 PHE Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 291 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 106 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 126 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 799 GLN ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 HIS G 288 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.108454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.084945 restraints weight = 35761.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.087796 restraints weight = 18322.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.089609 restraints weight = 11718.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.090870 restraints weight = 8721.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.091686 restraints weight = 7135.995| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.218 11857 Z= 0.291 Angle : 0.819 14.662 16107 Z= 0.422 Chirality : 0.050 0.277 1747 Planarity : 0.006 0.092 2112 Dihedral : 5.389 50.692 1650 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 4.67 % Allowed : 21.48 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.20), residues: 1482 helix: -2.67 (0.73), residues: 37 sheet: -2.04 (0.19), residues: 608 loop : -2.35 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 721 TYR 0.024 0.003 TYR C 471 PHE 0.033 0.003 PHE G 209 TRP 0.035 0.003 TRP C 133 HIS 0.012 0.003 HIS G 279 Details of bonding type rmsd covalent geometry : bond 0.00663 (11857) covalent geometry : angle 0.81932 (16107) hydrogen bonds : bond 0.04281 ( 323) hydrogen bonds : angle 7.18273 ( 915) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 161 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 5 THR cc_start: 0.7667 (m) cc_final: 0.7438 (p) REVERT: C 246 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8881 (tt) REVERT: C 451 MET cc_start: 0.9115 (tpp) cc_final: 0.8834 (tpp) REVERT: C 470 MET cc_start: 0.8164 (ttp) cc_final: 0.7726 (tmm) REVERT: C 602 TYR cc_start: 0.8443 (t80) cc_final: 0.8116 (t80) REVERT: D 115 TYR cc_start: 0.8903 (t80) cc_final: 0.8633 (t80) REVERT: D 121 LYS cc_start: 0.9264 (tttt) cc_final: 0.8905 (tptt) REVERT: D 152 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8386 (p) REVERT: K 30 LEU cc_start: 0.9084 (tp) cc_final: 0.8690 (mm) REVERT: K 66 GLU cc_start: 0.9113 (tp30) cc_final: 0.8703 (tp30) REVERT: K 92 GLU cc_start: 0.8985 (tt0) cc_final: 0.8710 (tp30) REVERT: K 112 ILE cc_start: 0.9224 (mm) cc_final: 0.8840 (mp) REVERT: K 130 ASN cc_start: 0.8609 (m-40) cc_final: 0.8304 (p0) REVERT: K 166 ASP cc_start: 0.8181 (t0) cc_final: 0.7967 (t70) REVERT: G 24 ILE cc_start: 0.8182 (mt) cc_final: 0.7848 (mm) REVERT: G 180 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.7972 (pm20) REVERT: G 196 ASN cc_start: 0.7861 (p0) cc_final: 0.7630 (p0) outliers start: 58 outliers final: 28 residues processed: 211 average time/residue: 0.0921 time to fit residues: 28.6862 Evaluate side-chains 173 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 206 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 209 PHE Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 291 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 48 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 85 optimal weight: 0.0770 chunk 40 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 93 HIS C 167 GLN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 ASN ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN K 36 HIS ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 243 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.111706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.088348 restraints weight = 35522.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.091357 restraints weight = 18109.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.093340 restraints weight = 11478.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.094630 restraints weight = 8404.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.095493 restraints weight = 6828.084| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11857 Z= 0.129 Angle : 0.667 8.672 16107 Z= 0.342 Chirality : 0.046 0.169 1747 Planarity : 0.005 0.072 2112 Dihedral : 4.998 52.676 1650 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.10 % Allowed : 23.41 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.20), residues: 1482 helix: -2.94 (0.69), residues: 39 sheet: -1.84 (0.20), residues: 593 loop : -2.26 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 158 TYR 0.031 0.002 TYR G 27 PHE 0.028 0.002 PHE G 209 TRP 0.039 0.002 TRP C 133 HIS 0.006 0.001 HIS G 228 Details of bonding type rmsd covalent geometry : bond 0.00284 (11857) covalent geometry : angle 0.66699 (16107) hydrogen bonds : bond 0.03291 ( 323) hydrogen bonds : angle 6.88395 ( 915) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 171 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 ARG cc_start: 0.9109 (tmm160) cc_final: 0.8698 (tmm-80) REVERT: C 246 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8923 (tt) REVERT: C 451 MET cc_start: 0.8929 (tpp) cc_final: 0.8377 (tpp) REVERT: C 470 MET cc_start: 0.8179 (ttp) cc_final: 0.7767 (ptm) REVERT: C 586 LEU cc_start: 0.8854 (mm) cc_final: 0.8504 (mt) REVERT: C 599 ASN cc_start: 0.9148 (m-40) cc_final: 0.8930 (m-40) REVERT: D 15 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6924 (mp0) REVERT: D 115 TYR cc_start: 0.8866 (t80) cc_final: 0.8616 (t80) REVERT: D 121 LYS cc_start: 0.9308 (tttt) cc_final: 0.8944 (tptt) REVERT: D 152 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.7901 (p) REVERT: K 30 LEU cc_start: 0.9006 (tp) cc_final: 0.8657 (mm) REVERT: K 58 TYR cc_start: 0.6806 (OUTLIER) cc_final: 0.6508 (p90) REVERT: K 66 GLU cc_start: 0.9050 (tp30) cc_final: 0.8595 (tp30) REVERT: K 92 GLU cc_start: 0.8918 (tt0) cc_final: 0.8623 (tp30) REVERT: K 112 ILE cc_start: 0.9210 (mm) cc_final: 0.8819 (mp) REVERT: K 130 ASN cc_start: 0.8636 (m-40) cc_final: 0.8296 (p0) REVERT: G 24 ILE cc_start: 0.7996 (mt) cc_final: 0.7655 (mm) REVERT: G 101 GLU cc_start: 0.8391 (pp20) cc_final: 0.8097 (pp20) REVERT: G 180 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.6853 (pm20) REVERT: G 196 ASN cc_start: 0.7867 (p0) cc_final: 0.7632 (p0) REVERT: G 230 ASP cc_start: 0.6830 (t0) cc_final: 0.6380 (t0) REVERT: G 279 HIS cc_start: 0.7950 (t-90) cc_final: 0.7707 (t70) outliers start: 51 outliers final: 25 residues processed: 211 average time/residue: 0.0969 time to fit residues: 29.5041 Evaluate side-chains 192 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 58 TYR Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 291 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 127 optimal weight: 20.0000 chunk 144 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 136 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 139 optimal weight: 0.9980 chunk 110 optimal weight: 30.0000 chunk 69 optimal weight: 0.0050 overall best weight: 2.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 232 ASN ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.109610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.086443 restraints weight = 35244.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.089363 restraints weight = 17780.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.091265 restraints weight = 11228.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.092507 restraints weight = 8235.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.093203 restraints weight = 6735.356| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 11857 Z= 0.175 Angle : 0.684 10.322 16107 Z= 0.348 Chirality : 0.046 0.167 1747 Planarity : 0.005 0.077 2112 Dihedral : 4.908 48.062 1650 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 4.67 % Allowed : 23.57 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.21), residues: 1482 helix: -2.79 (0.70), residues: 39 sheet: -1.73 (0.20), residues: 596 loop : -2.10 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 158 TYR 0.022 0.002 TYR C 720 PHE 0.026 0.002 PHE G 209 TRP 0.047 0.002 TRP C 133 HIS 0.007 0.002 HIS G 228 Details of bonding type rmsd covalent geometry : bond 0.00389 (11857) covalent geometry : angle 0.68370 (16107) hydrogen bonds : bond 0.03254 ( 323) hydrogen bonds : angle 6.57166 ( 915) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 158 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 5 THR cc_start: 0.7688 (m) cc_final: 0.7448 (p) REVERT: C 470 MET cc_start: 0.8211 (ttp) cc_final: 0.7767 (ptm) REVERT: C 586 LEU cc_start: 0.8852 (mm) cc_final: 0.8517 (mt) REVERT: D 115 TYR cc_start: 0.8914 (t80) cc_final: 0.8536 (t80) REVERT: D 121 LYS cc_start: 0.9307 (tttt) cc_final: 0.8946 (tptt) REVERT: D 141 TYR cc_start: 0.7469 (m-80) cc_final: 0.7058 (m-80) REVERT: D 152 THR cc_start: 0.8483 (OUTLIER) cc_final: 0.8193 (p) REVERT: K 30 LEU cc_start: 0.9002 (tp) cc_final: 0.8692 (mm) REVERT: K 58 TYR cc_start: 0.6879 (OUTLIER) cc_final: 0.6659 (p90) REVERT: K 66 GLU cc_start: 0.9036 (tp30) cc_final: 0.8574 (tp30) REVERT: K 92 GLU cc_start: 0.8950 (tt0) cc_final: 0.8602 (tp30) REVERT: K 112 ILE cc_start: 0.9188 (mm) cc_final: 0.8755 (mp) REVERT: K 130 ASN cc_start: 0.8591 (m-40) cc_final: 0.8284 (p0) REVERT: G 24 ILE cc_start: 0.8192 (mt) cc_final: 0.7825 (mm) REVERT: G 180 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7480 (pm20) REVERT: G 196 ASN cc_start: 0.7909 (p0) cc_final: 0.7533 (p0) REVERT: G 230 ASP cc_start: 0.6883 (t0) cc_final: 0.6579 (t0) REVERT: G 279 HIS cc_start: 0.8030 (t-90) cc_final: 0.7798 (t70) outliers start: 58 outliers final: 41 residues processed: 205 average time/residue: 0.0977 time to fit residues: 29.2912 Evaluate side-chains 195 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 151 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 206 PHE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 58 TYR Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 150 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 77 TYR Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 332 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 129 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 104 optimal weight: 0.0070 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 232 ASN ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.110878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.087328 restraints weight = 35144.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.090312 restraints weight = 17849.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.092283 restraints weight = 11338.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.093548 restraints weight = 8321.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.094208 restraints weight = 6789.424| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11857 Z= 0.136 Angle : 0.653 9.477 16107 Z= 0.332 Chirality : 0.045 0.162 1747 Planarity : 0.004 0.071 2112 Dihedral : 4.768 46.377 1650 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 4.59 % Allowed : 24.05 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.21), residues: 1482 helix: -2.78 (0.69), residues: 39 sheet: -1.62 (0.21), residues: 585 loop : -2.03 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 62 TYR 0.027 0.002 TYR C 720 PHE 0.026 0.001 PHE G 209 TRP 0.029 0.002 TRP C 133 HIS 0.007 0.001 HIS G 228 Details of bonding type rmsd covalent geometry : bond 0.00303 (11857) covalent geometry : angle 0.65326 (16107) hydrogen bonds : bond 0.02909 ( 323) hydrogen bonds : angle 6.41894 ( 915) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 153 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 246 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8927 (tt) REVERT: C 287 MET cc_start: 0.8684 (mmm) cc_final: 0.8433 (mmm) REVERT: C 359 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8339 (t) REVERT: C 470 MET cc_start: 0.8208 (ttp) cc_final: 0.7691 (tmm) REVERT: C 586 LEU cc_start: 0.8833 (mm) cc_final: 0.8484 (mt) REVERT: D 115 TYR cc_start: 0.8910 (t80) cc_final: 0.8640 (t80) REVERT: D 121 LYS cc_start: 0.9289 (tttt) cc_final: 0.8949 (tptt) REVERT: D 141 TYR cc_start: 0.7463 (m-80) cc_final: 0.7097 (m-80) REVERT: D 152 THR cc_start: 0.8379 (OUTLIER) cc_final: 0.8076 (p) REVERT: K 66 GLU cc_start: 0.9054 (tp30) cc_final: 0.8582 (tp30) REVERT: K 92 GLU cc_start: 0.8832 (tt0) cc_final: 0.8621 (tp30) REVERT: K 101 LYS cc_start: 0.9020 (mmtp) cc_final: 0.8515 (mmmt) REVERT: K 112 ILE cc_start: 0.9192 (mm) cc_final: 0.8768 (mp) REVERT: K 130 ASN cc_start: 0.8587 (m-40) cc_final: 0.8275 (p0) REVERT: K 149 TYR cc_start: 0.8632 (p90) cc_final: 0.8431 (p90) REVERT: G 24 ILE cc_start: 0.8019 (mt) cc_final: 0.7653 (mm) REVERT: G 180 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7452 (pm20) REVERT: G 196 ASN cc_start: 0.7882 (p0) cc_final: 0.7533 (p0) REVERT: G 230 ASP cc_start: 0.6900 (t0) cc_final: 0.6578 (t0) REVERT: G 279 HIS cc_start: 0.7801 (t-90) cc_final: 0.7526 (t70) outliers start: 57 outliers final: 38 residues processed: 200 average time/residue: 0.0877 time to fit residues: 25.8546 Evaluate side-chains 187 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 145 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 150 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 63 GLN Chi-restraints excluded: chain G residue 77 TYR Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 332 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 26 optimal weight: 0.0040 chunk 31 optimal weight: 40.0000 chunk 37 optimal weight: 9.9990 chunk 110 optimal weight: 0.4980 chunk 14 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 39 optimal weight: 0.0270 chunk 134 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 141 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 overall best weight: 2.9054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 GLN ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.108639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.085411 restraints weight = 35328.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.088304 restraints weight = 17789.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.090202 restraints weight = 11280.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.091411 restraints weight = 8295.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.092170 restraints weight = 6778.243| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11857 Z= 0.188 Angle : 0.675 10.932 16107 Z= 0.346 Chirality : 0.046 0.202 1747 Planarity : 0.005 0.079 2112 Dihedral : 4.849 42.712 1650 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 4.75 % Allowed : 24.62 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.21), residues: 1482 helix: -2.39 (0.73), residues: 39 sheet: -1.61 (0.21), residues: 588 loop : -1.92 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 62 TYR 0.026 0.002 TYR C 720 PHE 0.026 0.002 PHE K 26 TRP 0.061 0.002 TRP C 133 HIS 0.006 0.002 HIS G 239 Details of bonding type rmsd covalent geometry : bond 0.00415 (11857) covalent geometry : angle 0.67543 (16107) hydrogen bonds : bond 0.03023 ( 323) hydrogen bonds : angle 6.39489 ( 915) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 152 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 134 LEU cc_start: 0.8765 (mm) cc_final: 0.8323 (tp) REVERT: C 246 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8897 (tt) REVERT: C 470 MET cc_start: 0.8218 (ttp) cc_final: 0.7645 (tmm) REVERT: C 586 LEU cc_start: 0.8862 (mm) cc_final: 0.8532 (mt) REVERT: D 115 TYR cc_start: 0.8949 (t80) cc_final: 0.8728 (t80) REVERT: D 121 LYS cc_start: 0.9316 (tttt) cc_final: 0.8983 (tptt) REVERT: D 141 TYR cc_start: 0.7430 (m-80) cc_final: 0.7091 (m-80) REVERT: D 152 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8313 (p) REVERT: D 207 CYS cc_start: 0.8149 (p) cc_final: 0.7726 (t) REVERT: K 66 GLU cc_start: 0.8987 (tp30) cc_final: 0.8654 (tp30) REVERT: K 92 GLU cc_start: 0.8852 (tt0) cc_final: 0.8574 (tp30) REVERT: K 101 LYS cc_start: 0.9063 (mmtp) cc_final: 0.8543 (mmmt) REVERT: K 112 ILE cc_start: 0.9195 (mm) cc_final: 0.8781 (mp) REVERT: K 130 ASN cc_start: 0.8578 (m-40) cc_final: 0.8106 (p0) REVERT: K 149 TYR cc_start: 0.8621 (p90) cc_final: 0.7977 (p90) REVERT: G 24 ILE cc_start: 0.8198 (mt) cc_final: 0.7877 (mm) REVERT: G 180 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.7631 (pm20) REVERT: G 196 ASN cc_start: 0.7913 (p0) cc_final: 0.7594 (p0) REVERT: G 230 ASP cc_start: 0.7071 (t0) cc_final: 0.6711 (t0) REVERT: G 318 SER cc_start: 0.7662 (m) cc_final: 0.7324 (p) outliers start: 59 outliers final: 41 residues processed: 201 average time/residue: 0.0886 time to fit residues: 26.2812 Evaluate side-chains 193 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 206 PHE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 150 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 77 TYR Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 332 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 104 optimal weight: 10.0000 chunk 11 optimal weight: 0.0970 chunk 98 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 137 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 232 ASN ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.107788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.084390 restraints weight = 36201.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.087351 restraints weight = 18193.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.089272 restraints weight = 11522.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.090532 restraints weight = 8484.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.091305 restraints weight = 6959.179| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11857 Z= 0.193 Angle : 0.695 10.699 16107 Z= 0.355 Chirality : 0.046 0.183 1747 Planarity : 0.005 0.082 2112 Dihedral : 4.903 41.434 1650 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 4.10 % Allowed : 25.74 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.21), residues: 1482 helix: -2.50 (0.68), residues: 39 sheet: -1.59 (0.21), residues: 586 loop : -1.87 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 62 TYR 0.026 0.002 TYR C 720 PHE 0.027 0.002 PHE G 209 TRP 0.052 0.002 TRP C 133 HIS 0.022 0.002 HIS G 279 Details of bonding type rmsd covalent geometry : bond 0.00426 (11857) covalent geometry : angle 0.69452 (16107) hydrogen bonds : bond 0.03160 ( 323) hydrogen bonds : angle 6.42305 ( 915) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 150 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 246 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8883 (tt) REVERT: C 470 MET cc_start: 0.8249 (ttp) cc_final: 0.7671 (tmm) REVERT: C 586 LEU cc_start: 0.8874 (mm) cc_final: 0.8560 (mt) REVERT: D 15 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6719 (mp0) REVERT: D 74 ASP cc_start: 0.7594 (t0) cc_final: 0.7043 (t0) REVERT: D 121 LYS cc_start: 0.9314 (tttt) cc_final: 0.8980 (tptt) REVERT: D 141 TYR cc_start: 0.7629 (m-80) cc_final: 0.7394 (m-80) REVERT: D 152 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8298 (p) REVERT: D 197 TYR cc_start: 0.6598 (OUTLIER) cc_final: 0.5295 (t80) REVERT: D 207 CYS cc_start: 0.8207 (p) cc_final: 0.7743 (t) REVERT: K 66 GLU cc_start: 0.9086 (tp30) cc_final: 0.8811 (tp30) REVERT: K 92 GLU cc_start: 0.8955 (tt0) cc_final: 0.8650 (tp30) REVERT: K 101 LYS cc_start: 0.9070 (mmtp) cc_final: 0.8533 (mmmt) REVERT: K 112 ILE cc_start: 0.9153 (mm) cc_final: 0.8694 (mp) REVERT: K 130 ASN cc_start: 0.8708 (m-40) cc_final: 0.8188 (p0) REVERT: G 24 ILE cc_start: 0.8226 (mt) cc_final: 0.7898 (mm) REVERT: G 180 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.7440 (pm20) REVERT: G 196 ASN cc_start: 0.7978 (p0) cc_final: 0.7656 (p0) REVERT: G 230 ASP cc_start: 0.7006 (t0) cc_final: 0.6753 (t0) REVERT: G 318 SER cc_start: 0.7788 (m) cc_final: 0.7491 (p) outliers start: 51 outliers final: 42 residues processed: 191 average time/residue: 0.0891 time to fit residues: 25.3027 Evaluate side-chains 194 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 147 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 197 TYR Chi-restraints excluded: chain D residue 205 PHE Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 63 GLN Chi-restraints excluded: chain G residue 77 TYR Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 332 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 89 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 78 optimal weight: 20.0000 chunk 17 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 GLN C 232 ASN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.100644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.077268 restraints weight = 35920.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.079942 restraints weight = 18351.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.081691 restraints weight = 11811.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.082820 restraints weight = 8792.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.083557 restraints weight = 7272.969| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 11857 Z= 0.363 Angle : 0.850 10.227 16107 Z= 0.443 Chirality : 0.051 0.198 1747 Planarity : 0.006 0.116 2112 Dihedral : 5.603 36.965 1650 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 4.75 % Allowed : 25.74 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.21), residues: 1482 helix: -2.90 (0.62), residues: 39 sheet: -1.78 (0.20), residues: 604 loop : -2.08 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 721 TYR 0.038 0.003 TYR C 720 PHE 0.033 0.003 PHE K 26 TRP 0.065 0.004 TRP C 133 HIS 0.014 0.003 HIS G 279 Details of bonding type rmsd covalent geometry : bond 0.00794 (11857) covalent geometry : angle 0.84984 (16107) hydrogen bonds : bond 0.03786 ( 323) hydrogen bonds : angle 6.87048 ( 915) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 138 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 150 TYR cc_start: 0.9096 (p90) cc_final: 0.8857 (p90) REVERT: C 167 GLN cc_start: 0.8345 (tp-100) cc_final: 0.7631 (tp-100) REVERT: C 287 MET cc_start: 0.8596 (mmm) cc_final: 0.8358 (mmm) REVERT: C 451 MET cc_start: 0.8924 (tpt) cc_final: 0.8690 (tpp) REVERT: C 470 MET cc_start: 0.8224 (ttp) cc_final: 0.7665 (tmm) REVERT: D 74 ASP cc_start: 0.7904 (t0) cc_final: 0.7499 (t0) REVERT: D 121 LYS cc_start: 0.9293 (tttt) cc_final: 0.8994 (tptt) REVERT: D 141 TYR cc_start: 0.7649 (m-80) cc_final: 0.7322 (m-80) REVERT: D 152 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8579 (p) REVERT: D 197 TYR cc_start: 0.7198 (OUTLIER) cc_final: 0.5116 (t80) REVERT: D 207 CYS cc_start: 0.8171 (p) cc_final: 0.7768 (t) REVERT: K 66 GLU cc_start: 0.9056 (tp30) cc_final: 0.8796 (tp30) REVERT: K 92 GLU cc_start: 0.8943 (tt0) cc_final: 0.8731 (tp30) REVERT: K 101 LYS cc_start: 0.9162 (mmtp) cc_final: 0.8686 (mmmt) REVERT: K 112 ILE cc_start: 0.9185 (mm) cc_final: 0.8748 (mp) REVERT: K 130 ASN cc_start: 0.8754 (m-40) cc_final: 0.8145 (p0) REVERT: K 160 LYS cc_start: 0.5072 (mmmt) cc_final: 0.4153 (mmtt) REVERT: G 180 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.7659 (pm20) REVERT: G 196 ASN cc_start: 0.7859 (p0) cc_final: 0.7551 (p0) REVERT: G 318 SER cc_start: 0.7863 (m) cc_final: 0.7656 (p) outliers start: 59 outliers final: 40 residues processed: 187 average time/residue: 0.0901 time to fit residues: 24.9882 Evaluate side-chains 176 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 133 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 197 TYR Chi-restraints excluded: chain D residue 205 PHE Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 332 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 31 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 80 optimal weight: 0.0970 chunk 64 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 123 optimal weight: 0.0770 overall best weight: 1.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.106133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.083425 restraints weight = 36413.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.086268 restraints weight = 18320.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.088117 restraints weight = 11625.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.089308 restraints weight = 8533.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.089962 restraints weight = 7003.820| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11857 Z= 0.138 Angle : 0.712 10.523 16107 Z= 0.361 Chirality : 0.047 0.181 1747 Planarity : 0.005 0.077 2112 Dihedral : 5.054 41.159 1650 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.98 % Allowed : 27.51 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.21), residues: 1482 helix: -2.63 (0.66), residues: 39 sheet: -1.72 (0.21), residues: 578 loop : -1.93 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 62 TYR 0.021 0.002 TYR C 720 PHE 0.033 0.002 PHE G 209 TRP 0.040 0.002 TRP C 133 HIS 0.009 0.002 HIS G 279 Details of bonding type rmsd covalent geometry : bond 0.00308 (11857) covalent geometry : angle 0.71152 (16107) hydrogen bonds : bond 0.02957 ( 323) hydrogen bonds : angle 6.52920 ( 915) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 167 GLN cc_start: 0.8085 (tp-100) cc_final: 0.6738 (tp-100) REVERT: C 287 MET cc_start: 0.8624 (mmm) cc_final: 0.8348 (mmm) REVERT: C 451 MET cc_start: 0.8847 (tpt) cc_final: 0.8510 (tpp) REVERT: C 470 MET cc_start: 0.8230 (ttp) cc_final: 0.7703 (tmm) REVERT: C 586 LEU cc_start: 0.8877 (mm) cc_final: 0.8575 (mt) REVERT: D 74 ASP cc_start: 0.7771 (t0) cc_final: 0.7411 (t0) REVERT: D 121 LYS cc_start: 0.9308 (tttt) cc_final: 0.8996 (tptt) REVERT: D 141 TYR cc_start: 0.7469 (m-80) cc_final: 0.7201 (m-80) REVERT: D 152 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8357 (p) REVERT: D 197 TYR cc_start: 0.6598 (OUTLIER) cc_final: 0.4856 (t80) REVERT: D 207 CYS cc_start: 0.8172 (p) cc_final: 0.7718 (t) REVERT: K 66 GLU cc_start: 0.9082 (tp30) cc_final: 0.8795 (tp30) REVERT: K 92 GLU cc_start: 0.8872 (tt0) cc_final: 0.8626 (tp30) REVERT: K 101 LYS cc_start: 0.9107 (mmtp) cc_final: 0.8578 (mmmt) REVERT: K 112 ILE cc_start: 0.9192 (mm) cc_final: 0.8748 (mp) REVERT: K 130 ASN cc_start: 0.8647 (m-40) cc_final: 0.8093 (p0) REVERT: G 101 GLU cc_start: 0.8392 (pp20) cc_final: 0.8064 (pp20) REVERT: G 180 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.7495 (pm20) REVERT: G 230 ASP cc_start: 0.7108 (t0) cc_final: 0.6819 (t0) outliers start: 37 outliers final: 29 residues processed: 181 average time/residue: 0.1014 time to fit residues: 26.7186 Evaluate side-chains 177 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 197 TYR Chi-restraints excluded: chain D residue 205 PHE Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 63 GLN Chi-restraints excluded: chain G residue 77 TYR Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 291 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 48 optimal weight: 0.8980 chunk 70 optimal weight: 20.0000 chunk 133 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 140 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 ASN ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 129 HIS ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.107494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.084617 restraints weight = 36340.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.087598 restraints weight = 17898.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.089507 restraints weight = 11191.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.090740 restraints weight = 8201.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.091381 restraints weight = 6692.453| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.208 11857 Z= 0.252 Angle : 0.956 59.195 16107 Z= 0.529 Chirality : 0.048 0.339 1747 Planarity : 0.005 0.077 2112 Dihedral : 5.043 41.120 1650 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.22 % Allowed : 27.27 % Favored : 69.51 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.21), residues: 1482 helix: -2.65 (0.65), residues: 39 sheet: -1.71 (0.21), residues: 578 loop : -1.93 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 62 TYR 0.020 0.002 TYR C 471 PHE 0.031 0.002 PHE G 209 TRP 0.127 0.003 TRP C 133 HIS 0.007 0.001 HIS G 228 Details of bonding type rmsd covalent geometry : bond 0.00531 (11857) covalent geometry : angle 0.95591 (16107) hydrogen bonds : bond 0.02954 ( 323) hydrogen bonds : angle 6.52308 ( 915) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1870.27 seconds wall clock time: 33 minutes 15.55 seconds (1995.55 seconds total)